IMEP #131 Near-Shore Fish Habitat Research Concerns

[BlueChip]

IMEP #131
Bacterial Soil Studies and Climate Change – 1890's-1990's
"Understanding Science Through History"
Aquaculture and Near-Shore Fish Habitat Research Concerns
The Problem of Science and Fertilizer Fraud of the 1890s
(This is the Viewpoint of Tim Visel – It is not the viewpoint of the EPA
Long Island Sound Study CAC or Habitat Committees)
This is a delayed report – February 2018
Revised to October 2021

The views presented here are of Tim Visel -no other agency or organization
Tim Visel retired from The Sound School June 30, 2022

A Note From Tim Visel

In some previous posts, I mentioned the need of university recognition of grant funded employment.  This combined with the peer review credentials or previous "publish or perish" in the 1990's made many university durational hires "grant dependent."  Employment positions had limited funds (grants) but could provide opportunities for future employment.  These positions were often termed "soft money," because tenured track, public funded university positions or "hard funds" had declined.  The university currency that was required to gain recognition it seemed was both publishing and now the awarding of grants (principal investigator) to staff.  The need to publish has become so intense and the demand for methods to do so quickly created avenues that research articles could be printed for a fee.  These journals are often called "predatory" as they seek individuals with the need to publish.  Some science journals often do not maintain the usual peer review process (Journal of Shellfish Research, Vol. 35, No. 1-5, 2016, by Peter G. Beninger, Jeffrey Beall and Sandra E. Shumway, The Growing Menace of Predatory Journals).

I was fortunate to be able to attend the 9th International Conference on Shellfish Restoration in Charleston, South Carolina in 2006.  In the early 2000's, much interest had been expressed about shellfish restoration and I was there to bring into focus the importance of history.  It had been over a decade since my last international conference and wanted to highlight the importance of knowing a shellfish habitat history.  The title of my presentation was "Connecticut Shellfish Restoration Projects Linked to Estuarine Health."  The focus was on some failed restoration projects from incomplete understanding of habitat health.  Some concern was expressed that talking about unsuccessful trial or projects would harm obtaining any future grants.  Another concern was projects needed to solve problems or policy concerns as grant areas needed new research.  No one pays for "old data" was a comment made to me during a break at the conference. 

I enjoyed the conference and felt it was very much worthwhile but was surprised by how many of the conversations revolved around gaining grant funding.  Some were so intense it reminded me of running a business – terms of overhead, guidelines, budgets and pass-through funding were all parts of these discussions.  A lot had changed in over a decade as grants, it seemed, had become so much a part of university employment.  This aspect of obtaining funds to support university research was not new.  In fact, Nelson Marshall, a URI Oceanography professor in the early 1980's (a time I was working for the URI College of Resource Development), wrote about the increasing need of grants in his 1999 book titled "In the Wake of a Great Yankee Oceanographer."  Dr. Marshall mentions the increased need for grants on pg. 145 as to the decades before:

"Though the need to write proposals for our work is not new, the burden and the tension involved were not nearly as great." 

However, the intensity of the grant discussions was new to me.

Science Grants

I would like to bring into focus the concept of predatory grants and public policy reports based upon them.  A basic flaw exists – no requirement that include reviews of previous research (a legal type of discovery) termed "citation amnesia" be included.  Several grant-supported initiatives also appear to have both a funding bias and public policy agenda.  This is not a new problem as illustrated in Rachel Carson's book Silent Spring regarding the use of chemicals.

Silent Spring raised issues of bias in science or "the funding effect."  The public policy agenda is more obscure but follows a similar pattern, for example, highlighting the loss (extinction event) of a species to raise public concern or awareness.  If sufficient awareness is raised, it can influence the mechanism to provide grant funds or enact conservation regulations.  Many times, this process is beneficial and necessary; however, many times it is misused.  The example I use is the water quality initiatives around nitrate contamination.  Nitrate, a natural substance, was found to contaminate drinking water, mostly well water from shallow hand-dug wells in the 1930's.  This excess nitrate was linked to wells near cesspools and demonstrated the need of "city water," water delivered to homes in pipes.  It seems the concept of the possibility of drinking your neighbor's nitrate was not enough to cause the funds needed to provide that clean water to some dense populations.  It lacked a public policy punch – so "blue baby syndrome" was added in the 1940's.  This certainly now gained the attention of public health officials and publicity aimed at elected office holders.  The chance that heavily nitrate-contaminated water could replace so much oxygen that your young child (baby) could turn blue galvanized public opinion.  The hesitation to bring water mains into rural areas soon faded.  This happened along coastal Connecticut shore communities built to escape "city heat" on small plots of land as outhouses were transitioned to indoor plumbing.

Most of the Connecticut shoreline had some public water mains by 1960.  Putting in water mains so summer cottages built on small lots could have clean water did not have early political support.  Watershed programs I attended during my employment with three University Land Grant Colleges 1978 to 1990 – nitrate contamination was often connected to blue baby syndrome.  No one questioned the need to keep wells away from septic systems and no one asked how often blue baby nitrate syndrome had occurred.  Decades later, I looked into how blue baby syndrome had impacted water quality (nitrate) studies a century ago here and found little in the historical literature.  In fact, I was not able to locate one confirmed case in Connecticut.  So, I expanded my search into New England again, little in the way of documented cases.  Eventually, I found confirmed and suspected cases in the south and west connected to heavily contaminated hand-dug shallow wells on farms.  Much later, it was explained that this issue was used as a public policy wedge to gain grant funding support.  These funds were awarded for "public works" and directly controlled by legislative (elected) quasi-public boards.  Later, regulations were enacted for building wells and their distance from septic systems. 

The next century would see this process reversed "grants" proceeding policy.  Often, these grants had a position confirmation component, which is the grant request for proposals had a carefully detailed position statement.  Successful grant awards were linked to applicants carefully reviewing the grant guidelines, which often referred applicants back to the RFP position statement.  This grant process, in the end, left applicants little "research space" to report results that greatly differed from those presented in the RFP – at least if the opportunity for a second grant existed (my view, T. Visel).

While the 2016 Journal of Shellfish Research concerned predatory journals, I would like to introduce the negative aspect of public policy science from "predatory grants" and a narrowing of research periods.  It is sometimes referred to as "citation amnesia," the purposeful forgetting of past research.  It is a seldomly discussed form of research misconduct, but one growing in importance.  While I often focus on the absence of an accurate fisheries history, it is hard to point to a deliberate omission of specific state and federal records or reports.  This is complicated by a surge of policy papers formatted to resemble "science" as in journal articles.  After reviewing hundreds of these reports (most involving fish and shellfish habitats or fishing practices), it is easy to spot them.  They usually have no defined author but are placed on the Internet as the products of working groups, technical committees or partnerships.  They frequently do not have references available to the public, and those that do have them, may have a cost recovery – you need to pay to see them (even if the researchers were funded with taxpayer funds, T. Visel).  Other times, important references are no longer available to review.

The best example of "citation amnesia," or in legal terms, the absence of a creditable discovery process is the four-decade effort to transplant eelgrass.  This submerged aquatic vegetation has had many policy papers and reports placed on the Internet.  Eelgrass transplant programs have been promoted to civic groups, environmental organizations and citizen science volunteers.  Thousands of volunteer hours and millions of dollars have been spent in an effort to replace or restore eelgrass meadows.  Most of these efforts have failed, but this is often portrayed as something new or dangerous and often the basis of additional policy reports and then later needed "action plans."  Most of these projects have a human pollution or development connection.  The citation amnesia comes into view as researchers at The U.S. Fish and Wildlife Service in the 1940's wrote about the same poor eelgrass transplant results.  C. E. Addy wrote an eelgrass planting guide in 1947 – on pg. 17 is the following comment:

"In all, numerous attempts were made to re-establish eelgrass in local areas from Massachusetts to North Carolina by the government, private agencies and clubs.  No notable achievements were made in these plantings and many of them failed completely." 

And why did so many of the 1980's and 1990's efforts to replant eelgrass (a "true" flowering underwater grass) fail – many did not look at soil conditions.  When so many transplants did fail, the term "proper site conditions" is found.  If you see that phrase, think soil conditions.  It might seem odd that transplanting grass should "forget" some of the basic soil science studies associated with bacteria, as many of these happened over a century ago.  It was Homer Wheeler, once President of the University of Rhode Island, who studied bacterial communities that helped grass grow and what soil conditions to avoid (See Manures and Fertilizers: A Work of Reference for All Interested in the Scientific Aspects of Modern Farming 1913, and reprinted in 2019).  These bacterial soil references are available to researchers today, in fact, the turf industry has much soil bacterial research (See Cornell University Turf Science Research – it is excellent).  And it's just not historical information that was forgotten.  Citation or reference amnesia is found in modern, recent reports, even attributed to agencies that focused on soil science.  These reports reflect public policy initiatives tied to observations, which lead readers to consider only human-caused events.  Consider a 2006 report from The U.S. Department of Agriculture – Natural Resources Conservation Service (this agency used to be titled The Soil Conservation Service prior to 1994) NRCS Action Plan to Conserve Identified Priority Fish and Wildlife Species and Habitat in Maine, June, 2006.  This report linked the decline of eelgrass habitat (50%) to disease and recreational waterfront and commercial fishing vessels Section 2.2 Eelgrass, pg. 6.  In table 4, the top priority for eelgrass was "restoration of eelgrass through seeding or planting."  These statements are incomplete.  Most of the habitat loss of eelgrass was from climatic cycles – and planting eelgrass has (and often continues to be) a failed restoration practice, chiefly from ignoring (or forgetting) basic soil science.  Most of the shallow habitat eelgrass dieoff is from the sulfides that build up under eelgrass in heat.  The disease aspect is related to high temperature slime molds.  The eelgrass initiative could be the best case history for citation amnesia as so much historical reference was available in the printed literature as to the negative impacts of this monoculture - thick eelgrass growths.  The chemistry of eelgrass peat (compost) is missing from many eelgrass reports.  In heat, the habitat benefits of shallow eelgrass decline rapidly.  With warmer waters, the habitat observations during colder periods (1960's and 1970's) are not attainable because of bacterial sulfate metabolism.  This information is also available in the turf industry studies of grass root failure from sulfide.  This is more apt to occur in heat and is called black layer disease.  This also impacts eelgrass with the buildup of compost molds and fungus.  Many eelgrass papers do not mention bacteria levels in or near eelgrass in high heat conditions.

The amount of research available that mentions sulfide soil concern in the turf industry is extensive.  For marine grasses, sulfide is more of a concern from the amount of sulfate dissolved in sea water.  When it gets hot, bacterial action shifts to those bacteria that can utilize sulfate for oxygen.  This was studied by Selman Waksman in peat studies in the 1940's that some bacteria use sulfur compounds – some producing sulfide and a general increase in ammonia.  On page 91 of "The Peats of New Jersey and Their Utilization Part A, Waksman et al., 1942, Rutgers Agriculture Experiment Station, is found this segment – my comments (   ) T. Visel:

"The activities of anaerobic bacteria in the lower layers result in the production from cellulose ("ose" indicates sugar, T. Visel) of various gases rich in methane and in hydrogen; in sulfur containing bogs, hydrogen sulfide is another characteristic production of decomposition."

And further:

"Furthermore, the lack of nitrifying bacteria prevents the oxidation of the ammonia to nitrate."

And on pg. 110 is the problem of peat to form sulfuric acid and harms plants:

"The lowest layer of the peat and the surface of the underlying soil may contain substances such as sulfate and sulfuric acid, which are highly toxic to plants.  These are rendered harmless by addition of lime.  Even when a peat is well supplied with lime in the surface layers, it may contain toxic substances below.  These ordinarily occur not only in undrained bogs, as a result of the oxidation of the original iron sulfide or iron pyrites.  In contact with oxygen of the air, these form iron sulfate and sulfuric acid, both of which are soluble in water and become toxic."

Eelgrass and eelgrass peat are surrounded by sulfate dissolved in sea water.  It, therefore, survives in at times hostile plant habitats largely controlled by heat and succession by energy.  Heat impacts bacterial composting and oxygen availability.  This is the sulfide soil dead line that moves in response to heat.  When coastal residents smell sulfide (the odor of rotten eggs), it is a toxin to plants as well.

A massive dieoff of the blue mussel during a prolonged heat wave occurred in June 2021 off British Columbia (described as a heat dome).  It killed hundreds of people, billions of blue mussels as well as oysters.  Christopher Harley from the University of British Columbia recorded shore (rocks) temperature of 122oF – far above the point for a widespread habitat failure. With continued heat, cold water species, such as the blue mussel, have a doubtful shallow water future.  With a warming climate, the same could be said for eelgrass.  No one, it seemed, looked at whether the rise and fall of shallow water eelgrass was related to bacterial shifts from temperature. 

The eelgrass protection initiative is an example where the need of grants, public policy and political factors all combined to create a false description of the role of eelgrass in estuarine habitat quality.  The initiative lacked checks and balances of research, public policy and political funding that created a bias so large that it could be a case history example for decades to come – my view, Tim Visel.

Paid Chemists and Fertilizer Fraud

To prevent biased science, we can look to the creation of the nation's Agriculture Experiment Stations.  A century ago, the farm community asked for unbiased science in regards to the benefits of commercial fertilizers.  Many articles on the marketing of fake fertilizers can be found in printed reports of the Connecticut Board of Agriculture.

We have a similar case history of soil science in the agriculture history and its examination is relevant today with the problem of biased science reports, either predatory grants or predatory journals.  Key to the support of building Agriculture Experiment Stations over a century ago was fertilizer fraud.  It is this case history that provides the foundation for "honest science" and what can happen when promotions do not match performance.  This started in Connecticut in 1863 around fertilizers and claims that were misleading or fraudulent.  A century later, Rachel Carson would raise a similar issue of bias with contracted grant funds science.  Rachel Carson, 1963, with Silent Spring:

"When the scientific organization speaks, whose voice do we hear – that of science or of the sustaining industry?"

The Fertilizer Frauds of the 1860's

Over a century ago, Connecticut Farmers organized and developed proposals for a series of independent government supported analytical laboratories for the testing of fertilizers.  This was in part because of misrepresentation in the fertilizer industry.  The word misrepresentation does not clearly describe what had happened – fertilizer fraud and false claims were so pervasive the agriculture community asked for "honest science."  New England farmers suffered the worst as soils low in organic matter needed nourishment found in fertilizers of many types.  However, what was promised did not match what was purchased and Samuel W. Johnson proclaimed in an 1897 annual report of the Connecticut Agricultural Experiment Station at New Haven, CT, who was at the time the Agriculture Experiment Station Director {Johnson reviewed the first twenty years}:

"During this time, the adulterated of fraudulent fertilizer, that for twenty-five years previously, were common in our markets, have practically disappeared, and, as respects them, the intelligent farmer has been efficiently protected from deception and fraud."  {From Frontiers of Plant Science Newsletter of The Connecticut Agriculture Experiment Station, New Haven, CT, Vol. 53, No. 1, Fall 2000.} 

In fact, the chance for "honest science" was much of the basis for establishing the first Agricultural Experiment Station – its first mission gave farmers an accurate assessment of the nutritional value and chemical component of commercial fertilizers. This was very important to Connecticut farmers as the organic rich topsoil was very "thin" here only about 5 inches had accumulated in the 10,000 years since ice covered Connecticut. These soils contained little organic matter and were being depleted of organic residues by organized agriculture.  The farm community simply asked for "honest science" for fertilizer analysis.

Introduction to Soil Bacteria

New England farmers, in general, faced more recent glacial "soils" often thin of organic material, plant nutrients and at times, soil bacteria. Soils, as well as plants, need nourishment and what needed nourishment the most was oxygen requiring soil bacteria.  These bacteria could in time invade root issues enabling plants to take up nitrogen, a necessary plant nutrient in the form of nitrate and other ions, retained in the soil important to plant, health and growth.

The remains of the last glaciations left Connecticut with "impoverished" soils with only a thin layer of dark humus — the "rich" and agricultural capable top soil, as long as it was fed; crops could grow and healthy bacteria made that possible, when it wasn't habitats (crops) failed and agriculture suffered.  These saprophytic "good" bacteria also helped the plants access nitrogen from air and move across root tissues and a section of a book titled "An Introduction to Botany" (Haupt, 1946) helps describe this process:

"These bacteria like the saprophytic ones mentioned about that live free in the soil are unique in being able to absorb free nitrogen from the air in the soil and to fix it, that is to form nitrogenous compounds within their own cells.  After this process has gone on for a while, some of the nitrogenous material becomes available for use by the legume (plant)."  This is termed nitrogen fixing bacteria today."

But bacteria needed food themselves – organic matter. Farmers for centuries have sought to replace depletion of organics by adding them back into the soil.

The principal soil nourishment was, for centuries, animal waste (manure), which strived to replace both captured nutrients, those needed by plants and sugars (compost) that fed the bacteria (straw or hay) in the topsoil. Connecticut's farmers (and New England's as well) soon learned the hardship of Connecticut's thin glacier soils and the fraud created by those who wished to profit from it. Bogus "new prepared" fertilizers of all types and alterations were marketed and sold, cheating the farm communities of both their dollars and their trust.

Professor William H. Brewer speaking before the Connecticut Board of Agriculture made a plea for both organization and support against this science fraud in the fertilizer market. Science, it seemed even then, was up for sale by those unfortunately who took advantage of this great industry need.  The Connecticut Dairy industry here flourished after the Civil War, as southern agriculture farm communities slowly rebuilt a destroyed war-torn agricultural infrastructure.  Within a decade the dairy industry would dominate Connecticut's agricultural community by 1874 and so also the need to grow grass and obtain hay "fodder".  Connecticut's fields often needed fertilizer. These thin soils just could not yield commercial crops without replacement of organic nutrients.  The supply of fodder plant food for dairy cows was critical to milk production.

Speaking before the general meeting of the Connecticut Board of Agriculture on pg. 243 (1874-1875 Report) – The meeting minutes of May 27, 1874 reflects this statement by Professor Brewer (William Henry Brewer) who became chair of the Sheffield Scientific School's Agriculture department at Yale University in 1864. He studied abroad at the University of Heidelberg in Germany and saw the expansion of the German Agriculture Experiment Station System), he would help organize farmers to learn about the German Experiment Station system in 1872 but studied European plant diseases in France in 1857. My insertions are labeled as such (T. Visel):

"All of our feeders who have to buy large quantities of food know how rapidly the demand for fodder material, of one kind and another, is increasing.  It is easy enough to see, that if these matters are to be investigated, they must be investigated by somebody who gives his time to it, and who has a certain amount of authority.  Who were the persons who, until this State (Connecticut, T. Visel) took the part it did in the chemical analysis of commercial fertilizers, were generally accepted as authorities in regard to the composition of commercial fertilizers? They were three-quarters of the persons who are technically called "commercial chemists"; persons who may or may not have been good chemists, but persons to whom the making of analyses was their means of living, so to speak.  They were not independent of the persons who sold the materials, and sometimes not as honest — well, they had no honesty to spare, to say the least.  I may say here, that while science is a good thing, it does not necessarily make a man honest.  I have heard of dishonest men who were scientific, after all."

To respond to complaints about fertilizer "fraud," the Connecticut Agriculture community led by the dairy interests soon sought legislative "relief" in Connecticut's General Assembly.

The Connecticut Board of Agriculture started petitions to deliver to elected legislative officials in 1873.  In 1875, the petitions were again presented to the legislature with the New Haven Agriculture Experiment Station being authorized the same year – with an unbiased expected role in fertilizer analysis.

We recognize this effort now as the foundation of all the United States Agriculture Experiment Stations – with New Haven's example for the first in the nation, established the following legislature session in 1875 under the motto, "Putting Science to Work for Society." The Connecticut Agricultural Experiment Station continues today to use the same motto.  Science had moved beyond those that held a vested interest – or those who had paid scientists to promote their products.  Within two years of establishing the Connecticut Agricultural Experiment Station, New England farmers had "honest" evaluations of what fertilizer consisted of and its value to them.  Within a decade, the problem of fertilizer fraud was over.

Soil Bacteria Concerns – Again

The impact of organic matter to soil healthy would be raised again- almost a century later, over much the same concerns – the use of fertilizer and how soils can be sustained in agriculture.  Prior to 1978 much of the US Department of Agriculture research was about direct nutrient ion (chemical) supplement providing ions that plants needed in amounts that maximized crop yields. While this did improve yields, it depleted organic matter in the soil itself while reducing a soils ability to retain water. Other aspects looked at the soil bacterial health.

In 1979, the USDA was faced with an organized "living soil movement."  Cultivation was, in fact, at times disruptive to soil bacteria, and open to increased erosion and rapid carbon loss; the fact was oxygen was creating rapid organic matter loss in soils.  This was coupled with chemical use at times, which threatened bacteria – because manure crops were expensive (manure spreading was a cost, etc.).  Soils, which contained healthy soils rich in bacteria and other "microbial life," became nitrogen poor, from low organic matter.   It was the bacterial action of the root zone which enabled the plant to pass nutrient ions into its tissue.  Without natural nutrient ions chemical ions would be needed, which increased chemical usage.  The soil could still provide for crops, but the root zone of natural bacterial active ions was declining.  At first, this living soil movement (which later began the organic farming discussions) was initially dismissed by the USDA.

The use of chemical fertilizers was, at the time, promoted on "exhausted" and different soil types, which responded differently; those with "thin" soils, ions passed quickly into the water table from low CEC values. There just was not enough organic matter to keep ions in range of the roots.   Without organic matter, CEC levels declined, ions moved faster in soils.  Nutrient ions, including nitrogen, moved into watersheds and then into flowing water.  Organic matter compost took a back seat for soil concerns.  This was a concern as I had come from a composting 4-H and garden experiences.

When I was employed by the USDA in a Barnstable county position with the University of Massachusetts Cooperative Extension Service, we were then advised by the USDA not to respond to articles or questions about living soils. This of course had an opposite effect, "County Agents" was on almost every fertilizer (or pesticide container) and quickly sought out the articles which talked about soil health and the bacteria in the soil itself, especially articles in the Rodale Press. By 1980, the USDA, it seems faced an organized living soil movement so large it quickly organized its own study team. (The 1980 United States Department of Agriculture Study Team On Organic Farming 1980 – 94 pgs. – now available at the Alternative Farming Systems Information Center.) Under a constant stream of criticism about "dead soils" and lifeless soils, it seemed as though the nation's Department of Agriculture had, in some way, turned its back against the chief tenant of its very existence, the farm soil in the early 1970's.  It was difficult to believe this had happened growing up as I did, composting everything it seemed into family gardens (See IMEP #116-B and Victory Gardens).  However, chemical fertilizers were relatively cheap and much easier to apply.  The before and after treatment trials of application were hard to ignore.

A foreword to this July 1980 report contains this statement: "We in USDA are receiving increasing numbers of request for information and advice on organic farm practices." – Bob Bergland, Secretary of Agriculture, United States. And, the Preface thanked Robert Rodale, "For allowing us to have access to the results of the Rodale Press Survey of The New Farmer readers. This survey produced a great deal of valuable background information and has added depth and perspective to this report." Anson R. Bertrand, Director Science and Education USDA. One of the largest questions the study team (1979) addressed was "steady decline in soil productivity and tilth from excessive soil erosion and loss of organic matter." And, "The concept of the soil as a living system which must be "fed" in a way that does not restrict the activities of beneficial organisms necessary for recycling nutrients and producing humus is central to this definition." (pg. XIL) (Note humus is well decomposed organic matter; it is the bacterial residue of organic matter digestion, compost is partially decomposed organic matter, much of it still maintains plant cell walls.)

In ten years (August 23, 1981), a gathering of over a hundred people in Putney, Vermont (reported to be the farm of Samuel Kaymen's, a pioneer in organic agriculture) had humbled the USDA about soil health and organic farming.  Samuel Kaymen's approach to organic farms, a regional and local approach to farm markets, farm fresh and farmers markets are the things we see today and still today are changing beliefs and values about the environment. These are the terms of food security and food sustainability, and the basis is around the operation of food systems (Organic Farmers See Solution to Food Crisis, New York Times, August 24, 1981).

It would take another decade before science once again came to review the concept of fertilizer to soil types. There was, at the time, a bias toward commercial fertilizers, almost to the point of minimizing soil value and soil bacterial functions.  It was the bacteria to a large extent controlled how fertile a soil could be.  In the end, it could be said that soil knowledge and bacterial function were again important.  The same concept of soil health was evident in coastal habitats as well.

Fisheries and Ocean Science Studies Missing Bacteria Study of Marine Soils?

On October 25, 2018, John Hammond's theory of massive habitat shifts caused by the "New England Oscillation" we recognize as the NAO or North Atlantic Oscillation would be in print.  On October 26, 2018, I obtained a press release titled "Commercial Shellfish Landings Decline Likely Linked to Environmental Factors, Not Overfishing," authored by Clyde Mackenzie and Mitchel Tarnowski, detailed shellfish declines attributed to the NAO.  I was sorry that John Hammond did not live long enough to see the article.  From Commercial Fisheries Review Article, Vol. 80, No. 1 (Winter 2018) is this statement:

"A major change to the bivalve habitats occurred when the North Atlantic Oscillation (NAO) Index switched from negative during about 1950 to 1980, when winter temperatures were relatively cool, to positive, resulting in warmer winter temperatures from about 1982 until about 2003.  We suggest that this climate shift affected the bivalves and their associated enough to cause the declines" (See IMEP #45: Climate Change Habitat and Fisheries – Mr. Hammond's Habitat History Lesson, posted February 5, 2015, The Blue Crab ForumTM, Fishing, Eeling and Oystering thread).

If the NAO could change entire inshore fisheries in shallow water, could it not influence the shallow water soil chemistry as well?  Eelgrass, for example, at times, mixes with or overlaps shellfish habitats, and why Cape Cod shellfishers did not hold eelgrass in high esteem.  Could it not also be impacted by periods of heat and few storms (positive NAO phase) to periods of cold with many storms (negative NAO phase) as well?

We know, for example, that sulfide metabolism sulfides is softening salt marsh in high heat.  The impact of more sulfate dissolved in seawater is changing salt marsh peat chemistry (Simon C. Anisfeld of Yale University describes this impact in 2012 as part of a segment of Tidal Marsh Restoration – See Appendix #2).  In heat and sea level rise, sulfate metabolism by use of high heat-tolerant bacteria are known to waste hydrogen sulfide, a plant poison.  This initially softens the Spartina pattens dense peat, allowing root tissue to be consumed in heat and followed by a rise in sulfide.  Loosened plant particles now are washed away, lowering the marsh surface, which now allows more sulfate onto the marsh surface for sulfate bacteria to consume more peat.  The sulfide deadline (first described to me by John Hammond detailing raft culture of oysters in Oyster Pond River in 1962 (See William Shaw "Raft Culture Oysters in Massachusetts USGPO 1962 – it contains a nice section about Mr. Hammond's help) agrees with Charles Beebe's conversations about the East River salt marsh between the towns of Madison and Guilford.  The peat now sinks as a loose soft deposit forms above.  Mr. Beebe's marker for this sinking was a "cord in a row" (today known as "corduroy") road made along the East River into "School Meadow" referencing when the harvest of salt hay supported Guilford's public schools.  At low tide, a dredge cut revealed the log and slab wood was about four feet below the current marsh surface (See EC thread "Salt Marshes - A Climate Change Bacterial Battlefield" posted September 10, 2015, The Blue Crab ForumTM).  The marsh surface was sinking as sulfide toxins, once deep in peat, approach the surface killing Spartina patens. 

This same process happens under eelgrass peat, which is most susceptible to sulfide poisoning because it never gets exposed to atmospheric oxygen, making it dependent upon oxygen levels in seawater.  When water warms and oxygen levels drop (this is natural – the inverse solubility law), sulfide toxins can kill eelgrass.  It is a cycle and when compared to the 1880 to 1920 period follows a similar pattern.  The 1870's cold and stormy period was followed by rapid eelgrass expansion – followed by high heat dieoffs.  Storms of the 1930's and 1940's restored its expansion in the 1950's and 1960's only to again die off in the heat of the 1980's to 2000's.  To make matters worse, the combined impact of sea level rise (more sulfate) and climate warming (more sulfide) almost seemed to guarantee that eelgrass would die back or die out.  Areas that obtain more energy (not less) are deeper and cooler and have the last "clean and green" eelgrass in sandy soils while remaining eelgrass in loose stagnant soils looked bad (brown and furry) if not terrible.  [I am told that when Connecticut submitted a response to Public Act 01-115, January 2007, "An Assessment of The Impacts of Commercial and Recreational Fishing and Other Activities to Eelgrass in Connecticut's Waters and Recommendations for Management" (135 pages), no good pictures of eelgrass could be found for Connecticut – 2007 was a very hot period and most of the shallow water eelgrass had died off or "looked terrible."  As often the case, a picture of eelgrass was used in a light sandy soil rather than in a compost, frequently termed "black mayonnaise."  So one from New Hampshire (Portsmouth Harbor) was used on the cover page.  [It's actually a great picture showing "clean and green eelgrass" in sandy soil, just not Connecticut.]

Colder high energy periods would support better soil conditions for eelgrass but hot long periods of organic composting would create sulfide toxicity.  It seems logical, therefore, that high energy areas would tend to sweep away compost material before it could generate toxic sulfides.  Cold winters and cold winter storms would also rejuvenate shallow soils and improve eelgrass health.  Unfortunately, with a warming climate and a decline in cool weather, these habitat benefits are not attainable.

We may soon need to completely revisit some basic estuarine habitat concepts, the law of habitat succession, unbiased soil chemistry, sulfate metabolism (in heat and cold) species diversity and research integrity (misconduct as citation amnesia) and finally what is known or called the "funding effect" which is a bias associated with some aspects of funded research in our coastal zone.  A significant missing coastal research element was the concept of marine soil bacteria and nitrogen pathways as influencing soil health. (Much of the recent bias is the selection of eelgrass Zostera marina as a preferred habitat type without critical soil studies. – my view, T. Visel).

As farmers then realized a century ago those promoting fertilizer products, and researching their products had a bias of intent and delivery.  They wanted the public to purchase their product a century ago, regardless of the long-term impact or benefit.  Hundreds of acres of farmland fell victim to toxic fertilizers, such as coal dust mixed with slaughterhouse blood meal that left fields with sulfur, heavy metals and little to no soil nourishment benefit.  Coal is fossilized sapropel, which is the continued reduction [putrefaction] of organic matter and is accompanied by sulfur-reducing bacteria. (That is how sulfur got into coal.)  It is sapropel that, perhaps, is the best climate-induced habitat indicator we have for coastal marine soils (habitats); and a return to the toxic sulfur cycle compost of high heat. In periods of high heat and low storm activity, it tends to build up (sapropel) in shallow habitats, an indication of low oxygen levels.  In time this compost "suffocates" marine soils and contains species of bacteria that breathe sulfur, not oxygen.  It often contains a living vegetation crust – eelgrass.

This is where eelgrass research and its response to climate change is most noticeable.  Many of the eelgrass policy papers repeat observations made during a negative NAO (1960's and 1970's) period.  It is during this cold and stormy period marine soils were cultivated and any sulfur rich compost (sapropel) mixed with sand or washed away.  Sulfides leave a "grey water" tint to storm water and after a powerful Nor'easter, Long Island Sound waters were sometimes grey for several days (personal observations, T. Visel).  Eelgrass soon took advantage of this cultivated (and increased soil pore flow capacity) marine soil.  The storm energy into these marine soils was tremendous, and while many eelgrass meadows were destroyed, it left large areas of "new sand" that could obtain both shellfish sets and eelgrass seeds.  From the shellfish industry perspective, it was a race to see if clams could be harvested before eelgrass would suffocate them.  For eelgrass researchers, eelgrass grew thick and lush in sandy soils in the 1960's and 1970's.  Reports and photographs show eelgrass (I term the clean and green) healthy in cold, clear water with a sandy soil.  Many organisms took advantage of this structure – reef complex.  Eelgrass in shallow water has similar habitat functions as roots and branches in freshwater.  Some of the most quoted eelgrass research occurred during a negative NAO – cold, clear water rich in oxygen.  (This was a period in which the research community reported climate cooling – some even warned about a mini ice age – See Harry Van loon comments interview with Hans Von Storch, September 4, 2004.)  Some of the most referenced eelgrass observations are that of Gordon W. Thayer et al. "The Impact of Man on Seagrass Systems," American Scientist, Vol. 63, No. 3, pgs. 288-296.  It contains a direct climate feature as it lists sulfate reduction, which in heat sulfide kills eelgrass (warm water is naturally oxygen-poor while in cold water higher oxygen levels keep sulfide production low).  Following is an excerpt from the above referenced article as item #4, my comments (    ) Tim Visel:

4.  "The organic matter in the detritus and in decaying roots (eelgrass roots, T. Visel) initiates sulfate reduction and maintains an active sulfur cycle."

And its role as a compost builder #6:

6.  "The leaves retard currents and increase sedimentation (build a compost, T. Visel) of organic and inorganic materials around the plants."

It is this feature that caused concern in the shellfish sector.  I often use David Belding (a noted Massachusetts shellfish researcher) comments about the composting impact of eelgrass (as with terrestrial grasses) to shellfish populations.  His is so concise and direct – The Soft Shell Clam Industry of Massachusetts November 1930 – reprinted by the Barnstable County Cooperative Extension Service in 2004:

"Eelgrass as we have seen is fatal to a good clam bed.  Many productive beds would be quickly spoiled by eelgrass if it were not for constant digging.  The grass raises the surface of the bed above the normal level by bringing in silt, which smothers the clams."

The ability of eelgrass plants and roots to gather organic matter and produce sulfide has been studied by Danish researchers.  Eelgrass was observed to die off in a ring, similar to those often observed in turf (See Appendix #3).  These large rings on shallow waters of the Baltic Sea caused great public concern, first of illegal chemical dumping, bombs from World War II, or even space aliens.  Finally, an article in the Los Angeles Times by Deborah Netburn, February 3, 2014, titled "Mysterious Underwater Rings In The Baltic Sea Explained" ended possible explanations – it was sulfide poisoning:

"According to biologists Marianne Holmer from (the) University of Southern Denmark and Jens Borum from the University of Copenhagen, the rings are created because of a buildup of sulfide in the mud around the grass.  The sulfide, which is toxic to eelgrass, kills the grass in the center of the rings, but not the grass along the perimeter..."

Adding the concept of habitat (time) succession further explains a type of marine composting:

"Most of the mud in this area of the Baltic Sea is quickly washed away, but the strands of eelgrass trap the mud in their midst.  The mud seemed to exist only inside the circle, so only here the plants are attacked by poison said Holmer and Borum in a statement.  Eelgrass grows by stolons, which spread radially in all directions (like terrestrial species of crab grass, T. Visel).  So, what happens is the grass traps the mud, the mud kills the old, weaker grass in the center of the circle, but leaves the newer grass at the edge (with less time to compost the mud, T. Visel) of the circle to thrive."

This also explains why eelgrass over or near sapropel, a sulfide-rich marine compost, die off first in low energy bays and coves or those salt ponds with small inlets to the sea in heat perish.  High heat in shallow water drives composting chemistry to sulfide and explains why shallow, older eelgrass meadows die off first (the brown and furry eelgrass) and those in higher energy areas, eelgrass persists in washed or cultivated soils in deeper, more open areas.  Rings from sulfide toxicity can be found in terrestrial turf and even at times in desert conditions (See Appendix #3: New York Times, April 13, 2021 – Veronique Greenwood, Observatory, To Find Magic Behind 'Fairy Circles,' Researchers Try Digging a Little Deeper).

In shallow water in heat, eelgrass helps form the first sapropels – marine composts that purge ammonia and sulfides, very similar to sealed terrestrial composts on land.  The marine soils need to be recognized and reflect upon the roles of the bacteria that live in them. 

The bacteria that live in marine soils have three distinct characteristics, they can mobilize the chemical compound sulfate for oxygen and have the ability to live in salt and can live in very hot seawater.  Salt tolerance makes these bacterial strains important the formation of carbon rich sapropel.  By consuming organic matter (remineralization), plant nutrients are released into the water, including large amounts of ammonia.  The chemistry fuel for this process is the oxygen locked in the sulfur compound sulfate and that release sulfide as a waste toxic/residue hydrogen sulfide.  When this happens, an ammonia sulfide rich compost begins to form in the absence of elemental oxygen or becomes a sapropel.  In hot summers, coastal residents may notice these marsh or sulfide smells with the term "rotting eggs."

Eelgrass has many characteristics of terrestrial grasses; they tend to collect and hold organic matter.  Because at times, oxygen is limiting in marine soils, the filing of soil pores can be a negative factor to soil chemistry in extreme heat.  The ability of eelgrass to modify habitats and in doing so accumulate "fines" changes soil chemistry.  It is these fine particles that restrict pore soil circulation and in brackish water, seal soils with a compost. In Chesapeake Science, Vol. 14, No. 4, pages 258 to 269, December 1973: Robert Orth reports in an article titled, "Benthic Infauna of Eelgrass Zostera Marina Beds," on the impact of eelgrass to soil structure, on page 261 of the report is found this comment: "A dense bed of Zostera may effectively reduce wave action near the bottom by baffling, thus trapping and preventing removal of finer sediments."

In effect, eelgrass helps seal marine soils, and transitions them to a sulfur compost, toxic to many organisms in low oxygen conditions. This compost or sapropel can in time kill eelgrass and give rise to the terms live and dead bottoms in the eel spear fishery. – That would also give reference to dead or "live bottoms", which more correctly was "dead soil" in the clam and oyster fisheries (See The Clam and Oyster Soils, posted October 16, 2020 and January 9, 2020, The Blue Crab ForumTM, Fishing, Eeling and Oystering thread).  A dead soil is one in which the soil bacteria that exist in oxygen are largely absent. Sulfur reducing bacteria can live in a lower no oxygen zone and waste sulfides, a toxin to plant life.  This process also purges tremendous amounts of ammonia – a sealed compost in heat.

Terrestrial farmers had long tried to minimize "dead soils" by draining water-soaked soils allowing oxygen to penetrate them enabling oxygen-requiring bacteria to live. When that occurs, bacterial action allows nutrient ions to pass into root tissues of plants. A soaked soil eliminates this oxygen exchange and sulfur bacteria increase and waste sulfide into the soils, "killing it. In terms of plant life, it is now a dead soil.  Much the same process occurs in shallow marine soils, the same habitats labeled as "critical" or "essential" for fish and shellfish nursery functions.  When marine soils die, the sulfate metabolism process produces hydrogen sulfide, a known plant toxic, but it is also poisonous to fish and shellfish. Some of the first soils-sulfide studies and observations impacting submerged grasses of estuaries were conducted in Florida. It is today one of the most referenced studies for the relationship of sulfide to dieoffs of turtle grass (Thalassia testudinum) in shallow waters.

This is from a series of climate factors including high heat, less rainfall and lower oxygen.  Paul R. Carson Jr., "Relationship of Sediment Sulfide to Mortality of Thalassia testudinum, in Florida Bay (1994) Bulletin of Marine Science, 54 (31), 733-746. Carlson et al., Yarbro and Barber and also Mass Mortality of the Tropical Seagrass Thalassia testudinum, Robblee et al., 1987.

"Sediment sulfide data, collected in studies of Florida Bay seagrass dieoff the last 12 years, provides evidence of sulfide toxicity that high sulfide concentrations can kill turtle grass, a high sulfide level, albeit, is circumstantial evidence" -- See "The Influence of Sediment Sulfide on the Structure of South Florida Seagrass Communities," Paul R. Carlson. 

Sapropel is low in oxygen, the marine compost that accumulates during heat and in poor tidal "flushing" areas that, over time, becomes toxic.  Sulfur-reducing bacterial reduction (putrefaction) of organic matter in the absence of oxygen now is subject to sulfide formation and the production of ammonia.  For eelgrass habitat quality it is at times beneficial to dredge out sapropel deposits to improve tidal flushing and reduce oxygen shortfalls.  It is this sticky (these sulfur reducing bacteria cannot break down complex cellulose and leaf waxes) blue/black deposits (muck) that grab an oar, or crab net pole and even claims a shoe or boot.  It is not a preferred habitat type in warm waters in fact it vectors dangerous bacterial strains of the Vibrio family – some pathogenic to us and sea life, such as winter flounder fin rot and the source of lobster shell disease.

This is the "sticky bottoms" sapropel that fills in navigation channels, and is labeled as sticky on navigation charts, and once harvested for a hay field fertilizer as a top dressing of organics.  The rise of sapropel during the 1880-1920 extremely warm (hot) period was the source of the "black water" fish kills of the past century.  Removing these sulfide rich organic deposits is actually a way to reduce ammonia and the sulfuric acid washes after storms.  Evidence exists in the fisheries historical literature to actual habitat benefit from dredging and improving tidal circulation.  Those studies (habitat observations) are rarely mentioned today in the reviews of post dredging process.

It is the periods of extreme heat and little storm activity to which sapropels (dead bottoms) tend to grow – and mark low periods of winter flounder habitats. It is the chemical-biological processes of bacteria that impact habitat quality. Farmers noticed in the 1880-1920's period, horses would now sink into salt marshes while attempting to cut salt hay. Soft spots or even sink holes (termed pannes today) could develop in them as recorded by Nichols of the Torrey Botanical Organization bulletins. During this time, several warm winters were reputed to lead to "ice famines"- ice did not make up on New England ponds – in open water.  It was that hot here in the late 1890's.  (For readers, there are excellent write ups of ice famines, including the one in 1899 in electronic media files).

It was the "open" winters during this time 1880-1920 in which marshes did not freeze hard and duck hunters often sank into soft marshes – it's during the Great Heat 1880-1920 that LL Bean™ invented the "boot shoe."

Sulfur-reducing bacteria, or "SRB" naturally complex heavy metals (even mercury) and release metal sulfides as sulfate is mobilized which is not limiting in marine coastal waters. The presence of sulfur and mercury in coal is the natural chemical and biological bacterial result of the fossilization of composted Sapropel, both terrestrial and marine; and it is not given a habitat classification.  Sapropel is a marine compost that forms in warm waters and should be given its proper name and listed as a distinct habitat type.  In an effort to protect coastal resources coastal policies have been established or "sold" to the public that will yield little benefit, one of which concerns the formation of sapropel as a positive or healthy habitat – it is not.  It is a toxic habitat type in heat.

Recent coastal science has also had at times "no honesty to spare" to borrow Dr. Brewer's phrase from over a century ago (my view).  Bottom disturbance studies, eelgrass services, habitat mapping, nitrogen habitat indicators and now the blue carbon initiative share a bias of "snapshot ecology" as a short time frame of reference promotion as something good but, in reality, delivers little of the promised benefits long term — just as farmers faced a century ago with fertilizers.  We need to review habitat successional aspects of marine soil for temperature and energy in shallow waters of Long Island Sound for fish, shellfish and plant species (my view, T. Visel).




Appendix #1
Sulfate Metabolism Causes Salt Marshes to Sink
Biochemical Responses to Tidal Restoration Chapter 3
By Simon C. Anisfeld
Redox and Sulfide
Tidal Marsh Restoration 2012
Island Press, Roman & Burdick Society for Ecological Restoration

"Healthy tidal marshes are characterized by a redox system dominated by the sulfate-sulfide pair.  Because of abundant inputs of organic matter and poor exchange of oxygen into waterlogged sediments, electron acceptors such as oxygen, nitrate, iron III and manganese (IV) are quickly depleted.  This results in reducing conditions below the first centimeter or so and leads to the production of phytotoxic sulfide through the reduction of the sulfate that is abundant in seawater." (pg. 43)

[Note: The presence of nitrate to provide oxygen to some bacterial strains is sometimes referred to as "nitrate buffering" and the absence of nitrate as the "sulfide deadline." – T. Visel]

Appendix #2
New York Times, April 13, 2021 – Veronique Greenwood, Observatory – Findings, Events and More
THE GAME'S AFOOT
To Find Magic Behind 'Fairy Circles,' Researchers Try Digging a Little Deeper

"In the Australian outback, certain grasses grow in eerie rings, with ramparts of dusty green standing at the edge of wide circles of bare red dirt.  Often described as "fairly circles," these rings of spinifex grass resemble structures first spotted in Namibian desert, both creating enormous honeycomb patterns across the landscape that really pop out on aerial photos.  In Namibia, scientists have deployed cameras on fishing rods, observed termite colonies and even used mathematical models to try to explain how this phenomenon arises.
   A new study suggests that microbes living in the soil may contribute to the rings' formation in Australia, rendering the dirt within the ring hostile to new seedlings and the dirt beyond the ring hospitable.
   Spinifex grasses start out as small round hummocks, said Angela Moles, an ecologist and author of the new paper.  Then, as new seedlings sprout outward, the plants in the middle die, leading to the ring shape.  Researchers have explored whether the bare inner soil becomes depleted of nutrients; whether it is too dry or compacted for new growth; and whether insects might be destroying the spinifex.  But a consensus on what is driving the formation of rings has yet to emerge."

Appendix #3
WETLANDS OF CONNECTICUT
State Geological and Natural History Survey of Connecticut
by Kenneth J. Metzler
State Geological 6 Natural History Survey of Connecticut
&
Ralph W. Tiner
U.S. Fish & Wildlife Service
1992
CHAPTER 5.
Hydric Soils of Connecticut

Definition of Hydric Soil

Hydric soils have been declined by the U.S.D.A Soil Conservation Service (1987) as soil that is saturated, flooded, or ponded long enough during the growing season to develop anaerobic (no oxygen) conditions in the upper part of the soil. These criteria can be used to identify soils that are sufficiently wet to support the growth and regeneration of hydrophytes. These soils are either saturated and/or flooded long enough to affect the reproduction, growth, and survival of plants.  Plants growing in wetlands must adapt to anaerobic soil conditions and deal with the presence of reduced forms of manganese, iron, and possibly Sulphur, which are more toxic than their oxidized forms (Patrick, I983).

Soils that were formerly wet but that are now completely drained may not be hydric soils.  These soils must be checked in the field to verify that drainage measures are still functional under normal or design conditions.  Where drainage measures fail, soils can revert to hydric conditions.  This condition, however, can only be determined on site.

Major Categories of Hydric Soils

A build-up of organic matter in developing organic soils in Connecticut results from prolonged anaerobic soil conditions associated with long periods of flooding and/or continuous soil saturation during the growing season.  These growing conditions impede aerobic decomposition (or oxidation) of the organic materials entering the water/soil system such as leaves, stems and roots, and encourage their accumulation as peat or muck over time.  Like most organic soils, peats and mucks are very poorly drained, and water moves through them very slowly.  Organic soils typically form in waterlogged depressions where peat or muck deposits range from one foot to more than 30 feet in depth.
Organic soils can be subdivided into three groups based on the percent of the identifiable plant material in the soil: (1) muck (Saprist) where two-thirds or more of the material is decomposed and less than one-third is identifiable; (2) peat (Fibrist) with less than one-third decomposed and greater than two-thirds identifiable; and, (3) mucky peat or peaty muck (Hemist) where between one-third and two-thirds is both decomposed and identifiable.  For more information on organic soils, the reader is referred to Histosols: Their Characteristics, Classification, and Use (Aandahl et al., 1974).

In other situations, organic matter does not accumulate in sufficient quantities to be considered peat or muck, and here mineral soils have developed.  Some mineral soils do, however, have thick organic surface layers related to excess soil moisture for long periods from heavy seasonal rainfall and/or a high water table (Ponnamperuma, 1972).